From StrategyWiki, the free strategy guide and
walkthrough wiki

Game Play

You begin every stage in the center of the bottom floor.
Princess Sakura will be watching you from the center of the top of
the screen at all times, held in close proximity to the Catfish
Pirate.

Every stage contains eight enemies. At the beginning of the
stage, the enemies are distributed two per floor. Since the floors
are unbroken, the enemies can not drop down to a lower level until
you break the floors.

You can break the breakable segments of the floor by jumping
into them and hitting them with your head. When the floor breaks,
there is a chance that an item will appear. Collect the item for
points or power-ups, but do not collect the bombs.

After the first stage and until much later in the game, there
is always one enemy, known as the boss enemy, that is different and
much more aggressive than the rest of the enemies. This enemy
always starts out on the top floor.

From stage 19 through 21, the stage will contain a random mix
of every enemy in the game. After you finish stage 21, the game
will continue, but the stage enemy arrangements will start over
from the first level.

Because the boss enemy starts on the top floor, you can
postpone the moment when you actually need to confront it by not
breaking any of the segments of the highest floor until you have
defeated the lower six enemies. This makes it easier to deal with
the boss enemy.

The Pin Cell (100 Eyes in the arcade), and Kakutan enemies can
not be defeated unless they are stunned. You can stun enemies by
jumping on them or hitting them from below as you jump up. Some
enemies will stun themselves if they fall down on their own.

After a period of time, the Catfish Pirate will become
restless, and begin to drop bombs at you from the top of the
screen. The bombs will always detonate at your current height on
the screen. If you need to cross from one side or the other, it is
best to attempt that at one end of the floor or the other, not in
the middle.

If you remain on one level of the stage for too long, a flame
will appear and slowly hunt you down. It is far easier to avoid
this flame by traveling above or below it than attempting to jump
over the flame on the same level.

When you eliminate an enemy, the Tamashii spirit energy will
appear where the enemy was defeated. Collect them before they rise
off the top of the screen for bonus points. Because the stage ends
almost as soon as the final enemy disappears, it is difficult to
collect the eighth and final Tamashii.

When you finish the stage, you will be awarded bonus points for
every unit in the timer that remains, and for each Tamashii that
you collected.

Ninja Art

There are two ways to invoke the Ninja Art of giant frog
summoning; Either collect four extra lives from the broken floor
segments, or collect three distinct power-ups.

If you accomplish either of these feats, the giant frog
Gamapakun will appear. You will instantly appear on his back. You
will take control of Gamapakun and you can direct him left and
right, make him jump up, or tell him to drop down.

Gamapakun will eat any enemy that he encounters. You will earn
1000 points for every enemy eaten. You can complete the stage using
Gamapakun, unless you allow the timer to reach 0, at which time,
Gamapakun will disappear. You will receive a 10,000 point bonus for
good performance if you complete the stage with Gamapakun
quickly.

Remember that if you collect a third distinct power-up,
Gamapakun will appear in lieu of the effect that the third power-up
would have given you.

Bonus Stage

During regular game play, Princess Sakura will toss down one
Sakura petal per stage. The petal will float down to the floor,
drifting left and right.

If you manage to collect three such Sakura petals, you will be
sent to the bonus stage immediately following the completion of
your current stage.

In the first bonus stage, Ninjakun will appear on the bottom
floor, and the Catfish Pirate will be present on the top floor,
with no floors in between.

You can throw one ninja star at a time at the pirate. In
contrast, the pirate can toss down three fireballs. He will proceed
to move randomly about to the left and the right.

Your goal is to hit him with your ninja star while avoiding the
fireballs that he throws at you. If you hit him before time runs
out, you will be awarded 5000 points. At that time, Princess Sakura
will drop to your side, and hearts will rise above each of you.
Then normal game play will resume.

After the first bonus stage, it is possible that two or more
Catfish Pirates will appear on the top floor. You must defeat each
of them to complete the stage.